Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit

MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments

“…Intermediate resolution cryo-electron microscopy (cryo-EM) structures of Arx1 bound to the yeast 60S (pre-)ribosome were reported previously 13,15 , and finally refined to 3.4 Å resolution 14 . These cryo-EM reconstructions confirmed the structural homology to the MetAPs and visualized Arx1 in the same binding site on the ribosomal tunnel exit that was observed for a bacterial MetAP-ribosome complex in a low-resolution structure of >10 Å 16 .…”

Timing and Specificity of Cotranslational Nascent Protein Modification in Bacteria

“…SRP binds free ribosomes at uL23 and uL29 near the ribosome exit site (39,40) and, upon the emergence of a transmembrane domain (TMD) or signal sequence on the nascent polypeptide, further contacts bL32, uL22, and uL24, resulting in substantial overlaps with the PDF and MAP binding sites (4,29,40). The TF binding site on the ribosome spans uL22, uL23, and uL29, which partially overlaps with those of SRP, PDF, and MAP (4,41). SecA also contacts the ribosome via uL23 (31,32), where both SRP and TF can bind.…”

“…Emerging evidence shows that protein biogenesis begins early, while the nascent protein is still being synthesized by the ribosome. As a nascent polypeptide emerges from the ribosome tunnel exit, a variety of ribosome-associated protein biogenesis factors (RPBs) bind at overlapping docking sites near the tunnel exit and compete for the nascent protein to influence its folding, localization, maturation, and quality control (1)(2)(3)(4). Efficient and accurate selection of nascent proteins into their proper biogenesis pathways is crucial, but how this is achieved in the crowded environment of the ribosome exit site is not well understood.…”

“…NME is one of the earliest events encountered by nascent proteins during their biogenesis and could occur cotranslationally as soon as the nascent chain reaches 44 to 48 residues (25). Earlier works have demonstrated the interaction between the ribosome and the NME enzymes in bacteria and eukaryotes (3,4,(25)(26)(27)(28). Recent measurements showed that Escherichia coli PDF and MAP bind the ribosome with apparent equilibrium dissociation constants (K d ) of 1.8 μM and 2.4 μM, respectively (25,29).…”

“…Recent measurements showed that Escherichia coli PDF and MAP bind the ribosome with apparent equilibrium dissociation constants (K d ) of 1.8 μM and 2.4 μM, respectively (25,29). Ribosome binding of PDF is mediated by its C-terminal helix, which docks in a groove between uL22 and bL32 near the ribosome exit site (4,29). The same site also mediates ribosome binding of MAP via a positively charged loop at the periphery of the active site (refs.…”